Metadata-Version: 2.4
Name: af3io
Version: 26.10
Summary: Eclectic utilities for AlphaFold 3
Author-email: jurgjn <jurgjn@users.noreply.github.com>
License-Expression: Apache-2.0
Project-URL: repository, https://github.com/jurgjn/af3io
Project-URL: changelog, https://github.com/jurgjn/af3io/blob/main/CHANGELOG.md
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.13
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: click
Requires-Dist: humanfriendly
Requires-Dist: scipy
Requires-Dist: pandas
Requires-Dist: zarr
Requires-Dist: biopython
Requires-Dist: pyarrow
Requires-Dist: backports.zstd; python_version < "3.14"
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Requires-Dist: pooch; extra == "test"
Dynamic: license-file

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# af3io
Collection of eclectic utilities for AlphaFold 3:
- Copy data pipeline output from existing results: [datafill.ipynb](examples/datafill/datafill.ipynb) ([open in Colab](https://colab.research.google.com/github/jurgjn/af3io/blob/main/examples/datafill/datafill.ipynb))
- Differences between input JSON files: [input_diff.ipynb](examples/input_diff/input_diff.ipynb) ([open in Colab](https://colab.research.google.com/github/jurgjn/af3io/blob/main/examples/input_diff/input_diff.ipynb))
- Set the `name` attribute of input JSONs to match their file names: `af3io fixname inputs/*.json` (use `--check` to only report mismatches)
- Collect summary confidences and interface scores (ipSAE, LIS, pDockQ, ...) from output directories or zip files, including predictions nested in other archives (tar, zip, gzip, zstd): `af3io summary-confidences predictions/ pools_5k.tar summary_confidences.parquet`
- Compress confidences JSONs (experimental): [confidences-compress.ipynb](examples/confidences-compress/confidences-compress.ipynb) ([open in Colab](https://colab.research.google.com/github/jurgjn/af3io/blob/main/examples/confidences-compress/confidences-compress.ipynb))
